System Analysis and Nematode Phylogeny
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(Stsm) Scientific Report
SHORT TERM SCIENTIFIC MISSION (STSM) SCIENTIFIC REPORT This report is submitted for approval by the STSM applicant to the STSM coordinator Action number: CA15219-45333 STSM title: Free-living marine nematodes from the eastern Mediterranean deep sea - connecting COI and 18S rRNA barcodes to structure and function STSM start and end date: 06/02/2020 to 18/3/2020 (short than the planned two months due to the Co-Vid 19 virus pandemic) Grantee name: Zoya Garbuzov PURPOSE OF THE STSM: My Ph.D. thesis is devoted to the population ecology of free-living nematodes inhabiting deep-sea soft substrates of the Mediterranean Levantine Basin. The success of the study largely depends on my ability to accurately identify collected nematodes at the species level, essential for appropriate environmental analysis. Morphological identification of nematodes at the species level is fraught with difficulties, mainly because of their relatively simple body shape and the absence of distinctive morphological characters. Therefore, a combination of morphological identification to genus level and the use of molecular markers to reach species identification is assumed to provide a better distinction of species in this difficult to identify group. My STSM host, Dr. Nikolaos Lampadariou, is an experienced taxonomist and nematode ecologist. In addition, I will have access to the molecular laboratory of Dr. Panagiotis Kasapidis. Both researchers are based at the Hellenic Center for Marine Research (HCMR) in Crete and this STSM is aimed at combining morphological taxonomy, under the supervision of Dr. Lampadariou, with my recently acquired experience in nematode molecular taxonomy for relating molecular identifiers to nematode morphology. -
Taxonomy Assignment Approach Determines the Efficiency of Identification of Metabarcodes in Marine Nematodes
Taxonomy assignment approach determines the efficiency of identification of metabarcodes in marine nematodes Oleksandr Holovachov1, Quiterie Haenel2, Sarah J. Bourlat3 and Ulf Jondelius1 1Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden 2Zoological Institute, University of Basel, Switzerland 3Department of Marine Sciences, University of Gothenburg, Sweden Abstract: Precision and reliability of barcode-based biodiversity assessment can be affected at several steps during acquisition and analysis of the data. Identification of barcodes is one of the crucial steps in the process and can be accomplished using several different approaches, namely, alignment-based, probabilistic, tree-based and phylogeny-based. Number of identified sequences in the reference databases affects the precision of identification. This paper compares the identification of marine nematode barcodes using alignment-based, tree-based and phylogeny-based approaches. Because the nematode reference dataset is limited in its taxonomic scope, barcodes can only be assigned to higher taxonomic categories, families. Phylogeny-based approach using Evolutionary Placement Algorithm provided the largest number of positively assigned metabarcodes and was least affected by erroneous sequences and limitations of reference data, comparing to alignment- based and tree-based approaches. Key words: biodiversity, identification, barcode, nematodes, meiobenthos. 1 1. Introduction Metabarcoding studies based on high throughput sequencing of amplicons from marine samples have reshaped our understanding of the biodiversity of marine microscopic eukaryotes, revealing a much higher diversity than previously known [1]. Early metabarcoding of the slightly larger sediment-dwelling meiofauna have mainly focused on scoring relative diversity of taxonomic groups [1-3]. The next step in metabarcoding: identification of species, is limited by the available reference database, which is sparse for most marine taxa, and by the matching algorithms. -
International Conference on Biodiversity, Ecology and Conservation of Marine Ecosystems 2015
BECoME 2015 International Conference on Biodiversity, Ecology and Conservation of Marine Ecosystems 2015 PROGRAMME & ABSTRACT 1-4 June 2015 The University of Hong Kong Organizers: Sponsor: About BECoME2015 International Conference on Biodiversity, Ecology and Conservation of Marine Ecosystems 2015 (BECoME 2015) 1-4 June 2015 Hong Kong Programme and Abstracts Principal sponsors: Environment and Conservation Fund, The Government of the Hong Kong Special Administrative Region, China The Croucher Foundation, Hong Kong Sponsors: The Swire Group Charitable Trust, Hong Kong Ocean Park Conservation Fund, Hong Kong Ecosystems Limited Garland Science, Taylor & Francis Group The Marine Biological Association of Hong Kong Organizers: School of Biological Sciences and The Swire Institute of Marine Science, The University of Hong Kong Contents CONTENTS Preface ......................................................................................................................................... i Acknowledgements ................................................................................................................ v Organizing Committee .......................................................................................................... vi Invited Keynote Speakers .................................................................................................... vii Points to Note for Oral & Poster Presentations ................................................................. ix Programme ............................................................................................................................... -
A Focus on the Enoplida and Early-Branching Clades
University of New Hampshire University of New Hampshire Scholars' Repository Hubbard Center for Genome Studies (HCGS) Research Institutes, Centers and Programs 11-12-2010 Moving towards a complete molecular framework of the Nematoda: a focus on the Enoplida and early-branching clades Holly M. Bik Natural History Museum, London P. John D. Lambshead National Oceanography Centre W. Kelley Thomas University of New Hampshire, [email protected] David H. Lunt University of Hull Follow this and additional works at: https://scholars.unh.edu/hubbard Part of the Ecology and Evolutionary Biology Commons Recommended Citation Bik et al.: Moving towards a complete molecular framework of the Nematoda: a focus on the Enoplida and early-branching clades. BMC Evolutionary Biology 2010 10:353. This Article is brought to you for free and open access by the Research Institutes, Centers and Programs at University of New Hampshire Scholars' Repository. It has been accepted for inclusion in Hubbard Center for Genome Studies (HCGS) by an authorized administrator of University of New Hampshire Scholars' Repository. For more information, please contact [email protected]. Bik et al. BMC Evolutionary Biology 2010, 10:353 http://www.biomedcentral.com/1471-2148/10/353 RESEARCH ARTICLE Open Access Moving towards a complete molecular framework of the Nematoda: a focus on the Enoplida and early-branching clades Holly M Bik1,2,3*, P John D Lambshead2, W Kelley Thomas3, David H Lunt4 Abstract Background: The subclass Enoplia (Phylum Nematoda) is purported to be the earliest branching clade amongst all nematode taxa, yet the deep phylogeny of this important lineage remains elusive. -
Outcrossing and Parasitism in the Nematode Phylum
BRIEF COMMUNICATION doi:10.1111/evo.12565 A phylogenetic test of the Red Queen Hypothesis: Outcrossing and parasitism in the Nematode phylum Amanda Kyle Gibson1,2 and Jesualdo Arturo Fuentes1 1Department of Biology, Indiana University, Bloomington, Indiana 47405 2E-mail: [email protected] Received May 7, 2014 Accepted November 6, 2014 Sexual outcrossing is costly relative to selfing and asexuality, yet it is ubiquitous in nature, a paradox that has long puzzled evolutionary biologists. The Red Queen Hypothesis argues that outcrossing is maintained by antagonistic interactions between host and parasites. Most tests of this hypothesis focus on the maintenance of outcrossing in hosts. The Red Queen makes an additional prediction that parasitic taxa are more likely to be outcrossing than their free-living relatives. We test this prediction in the diverse Nematode phylum using phylogenetic comparative methods to evaluate trait correlations. In support of the Red Queen, we demonstrate a significant correlation between parasitism and outcrossing in this clade. We find that this correlation is driven by animal parasites, for which outcrossing is significantly enriched relative to both free-living and plant parasitic taxa. Finally, we test hypotheses for the evolutionary history underlying the correlation of outcrossing and animal parasitism. Our results demonstrate that selfing and asexuality are significantly less likely to arise on parasitic lineages than on free-living ones. The findings of this study are consistent with the Red Queen Hypothesis. Moreover, they suggest that the maintenance of genetic variation is an important factor in the persistence of parasitic lineages. KEY WORDS: Asexual reproduction, continuous-time Markov model, host–parasite coevolution, selfing, sexual outcrossing, stochastic character mapping. -
USING MOLECULAR TECHNIQUES to INVESTIGATE SOIL INVERTEBRATE COMMUNITIES in TEMPERATE FORESTS a Thesis Submitted to Kent State Un
USING MOLECULAR TECHNIQUES TO INVESTIGATE SOIL INVERTEBRATE COMMUNITIES IN TEMPERATE FORESTS A thesis submitted To Kent State University in partial Fulfillment of the requirements for the Degree of Master of Science By Dean James Horton December, 2015 © Copyright All rights reserved Thesis written by Dean James Horton B.S., Kent State University, 2012 M.S., Kent State University, 2015 Approved by Christopher B. Blackwood, Associate Professor, Ph.D., Department of Biological Sciences, Thesis Co-Advisor Mark W. Kershner, Associate Professor, Ph.D., Department of Biological Sciences, Thesis Co- Advisor Laura G. Leff, Chair Professor, Ph.D., Department of Biological Sciences James L. Blank, Dean, Ph.D., College of Arts and Sciences TABLE OF CONTENTS I. LIST OF FIGURES …………………………………….…………………… vi II. LIST OF TABLES ……………………………………..…………………….. x III. DEDICATION ………………………………………….………………….. xii IV. ACKNOWLEDGEMENTS ……………………………………………...... xiii V. CHAPTERS 1. GENERAL INTRODUCTION ………………………...………………... 1 REFERENCES …………………………………………..………………. 4 2. A PRIMER COMPARISON FOR MOLECULAR IDENTIFICATION OF INVERTEBRATE TAXA FROM SOIL AND LEAF LITTER ENVIRONMENTAL DNA ………………………………..…………… 11 1. ABSTRACT ………………………………………………………... 11 2. INTRODUCTION ………………………………………………….. 11 3. METHODS …………………………………………………………. 14 3.1. INDIVIDUAL VOUCHER SPECIMEN COLLECTION…….... 14 3.2. PRIMER TESTING ON INVERTEBRATE VOUCHER SPECIMENS………………………………………………...….. 14 3.3. eDNA IN ENVIRONMENTAL SAMPLES…………………… 16 4. RESULTS…………………………………………………………... 17 4.1. INVERTEBRATE VOUCHER SPECIMENS…………………. 17 4.2. ENVIRONMENTAL SOIL AND LEAF SAMPLES……….…. 18 5. DISCUSSION………………………………………………………. 19 iii 6. REFERENCES……………………………………………………… 21 3. HIGH-THROUGHPUT SEQUENCING REVEALS HIGH SOIL FAUNAL DIVERSITY AND SMALL-SCALE COMMUNITY TURNOVER IN TEMPERATE FORESTS…………………………….. 33 1. ABSTRACT………………………………………………………… 33 2. INTRODUCTION………………………………………………...… 34 3. METHODS…………………………………………………………. 38 3.1. STUDY AREA AND SAMPLING DESIGN………………..… 38 3.2. COMMUNITY CHARACTERIZATION……………..…….…. 39 3.3. DATA ANALYSIS…………………………………………..… 41 3.3.1. -
Free-Living Marine Nematodes from San Julián Bay (Santa Cruz, Argentina)
A peer-reviewed open-access journal ZooKeys 489: 133–144Free-living (2015) marine nematodes from San Julián Bay (Santa Cruz, Argentina) 133 doi: 10.3897/zookeys.489.7311 DATA PAPER http://zookeys.pensoft.net Launched to accelerate biodiversity research Free-living marine nematodes from San Julián Bay (Santa Cruz, Argentina) Catalina Pastor de Ward1, Virginia Lo Russo1, Gabriela Villares1, Viviana Milano2, Lidia Miyashiro3, Renato Mazzanti3 1 Laboratorio de Meiobentos CENPAT-CONICET, Boulevard Brown 2915, U9120ACF, Puerto Madryn, Argentina 2 Universidad Nacional de la Patagonia San Juan Bosco, sede Puerto Madryn. Boulevard Brown 3051, U9120ACF, Puerto Madryn, Argentina 3 Centro de Cómputos CENPAT-CONICET, Boulevard Brown 2915, U9120ACF, Puerto Madryn, Argentina Corresponding author: Catalina Pastor de Ward ([email protected]) Academic editor: P. Stoev | Received 19 February 2014 | Accepted 10 March 2015 | Published 24 March 2015 http://zoobank.org/C0480572-4990-46A1-B652-3BB35D4A6715 Citation: Pastor de Ward C, Lo Russo V, Villares G, Milano V, Miyashiro L, Mazzanti R (2015) Free-living marine nematodes from San Julián Bay (Santa Cruz, Argentina). ZooKeys 489: 133–144. doi: 10.3897/zookeys.489.7311 Abstract The free-living marine nematodes of San Julián Bay dataset is based on sediment samples collected in January 2009 during the project PICT AGENCIA-FONCYT 2/33345-2005. A total of 36 samples have been taken at three locations in the San Julián Bay, Santa Cruz Province, Argentina on the coastal littoral at three tidal levels. This presents a unique and important collection for the nematode benthic biodiversity assessment as this area remains one of the least known regions in Patagonia. -
Nematode Soil Community Structure and Function As a Bio-Indicator Of
I Nematode soil community structure and function as a bio-indicator of soil health in Fynbos and deciduous fruit orchards by Caro Kapp Thesis presented in fulfilment of the requirements for the degree of Master of Agricultural Sciences in the Faculty of Conservation Ecology and Entomology at Stellenbosch University Supervisor: Dr A.P. Malan Co-supervisors: Dr P. Addison and Ms S.G. Storey March 2013 Stellenbosch University http://scholar.sun.ac.za II Declaration By submitting this thesis/dissertation electronically, I declare that the entirety of the work contained therein is my own, original work, that I am the sole author thereof (save to the extent explicitly otherwise stated), that reproduction and publication thereof by Stellenbosch University will not infringe any third party rights and that I have not previously in its entirety or in part submitted it for obtaining any qualification. March 2013 Copyright © 2013 Stellenbosch University All rights reserved Stellenbosch University http://scholar.sun.ac.za III Acknowledgements I wish to express my heartfelt appreciation and gratitude to the following persons and institutions: My supervisors Dr. A.P. Malan and Mrs. S.G. Storey for their guidance, interest, support and constructive criticism during the course of this study. N. Ntushelo and M. Booyse, Biometry division Agricultural Research Council Infruitec-Nietvoorbij, Stellenbosch, for assistance with statistical advice and analyses. Dr. A. Swart, Dr. E. Marais and Dr. E van den Berg from the National Collection of Nematodes, Biosystematics Division, Agricultural Research Council, Plant Protection Research Institute, Pretoria for training in the identification of nematodes. Mr. B. Gilson, Mr. -
PSAMMONALIA the Newsletter of the International Association Of
PSAMMONALIA The Newsletter of the International Association of Meiobenthologists Number 168, December 2017 Composed and Printed at Lab. of Coastal Benthic Ecology P.P. Shirshov Institute of Oceanology RAS DONT FORGET TO RENEW YOUR MEMBERSHIP IN IAM! THE APPLICATION CAN BE FOUND AT: http://www.meiofauna.org/appform.html This newsletter is mailed electronically. Paper copies will be sent only upon request This Newsletter is not part of the scientific literature for taxonomic purposes 1 Executive Committee Vadim Mokievsky, Chairperson P.P. Shirshov Institute of Oceanology, Russian Hanan Mitwally (term expires 2019) Academy of Sciences, 36 Nakhimovskiy Faculty of Science, Oceanography, University of Prospect, 117218 Moscow, Russia. Alexandria, Moharram Bay, 21151, Egypt . [email protected] [email protected] Wonchoel Lee, Past Chairperson Gustavo Fonseca (term expires 2019) Lab Of Biodiversity, (#505), Department of Life Universidade Federal de São Paulo, Instituto do Science, College of Natural Sciences, Hanyang Mar, Av. AlmZ Saldanha da Gama 89, 11030- University, Seoul, South Korea. 400 Santos, Brazil. [email protected] [email protected] Daniel Leduc (term expires 2022) Ann Vanreusel, Treasurer National Institute of Water and Atmospheric Lab Morphologie, Universiteit Gent, Research, Private Bag 14-901, Wellington, New Ladengancjstraat 35, B-9000 Gent, Belgium. Zealand. [email protected] [email protected] Nabil Majdi (term expires 2022) Jyotsna Sharma, Assistant Treasurer Bielefeld University, Animal Ecology, Department of Biology, University of Texas at Konsequenz 45, 33615, Bielefeld, Germany. San Antonio, San Antonio, TX 78249-0661, [email protected] USA. [email protected] Ex-Officio Executive Committee (Past Chairpersons) • 1966-67 Robert Higgins - Founding Editor • 1987-89 John Fleeger • 1968-69 W. -
Meldal Et Al 2007 Phylogeny Nema.Pdf
Molecular Phylogenetics and Evolution 42 (2007) 622–636 www.elsevier.com/locate/ympev An improved molecular phylogeny of the Nematoda with special emphasis on marine taxa Birgit H.M. Meldal a,b,¤,1, Nicola J. Debenham b, Paul De Ley c, Irma Tandingan De Ley c, Jacques R. VanXeteren d, Andy R. Vierstraete d, Wim Bert d, Gaetan Borgonie d, Tom Moens e, Paul A. Tyler a, Melanie C. Austen f, Mark L. Blaxter g, Alex D. Rogers h, P.J.D. Lambshead b,¤ a School of Ocean and Earth Science, Southampton Oceanography Centre, University of Southampton, Waterfront Campus, European Way, Southampton SO14 3ZH, UK b Nematode Research Group, Department of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, UK c Department of Nematology, University of California, Riverside, CA 92521, USA d Department of Biology, and Centre for Molecular Phylogeny and Evolution, Ghent University, Ledeganckstraat 35, 9000 Ghent, Belgium e Marine Biology Section, Department of Biology, Ghent University, Krijgslaan 281/S8, 9000 Ghent, Belgium f Plymouth Marine Laboratory, Prospect Place, West Hoe, Plymouth PL1 3DH, UK g Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, King’s Buildings, West Mains Road, Edinburgh EH9 3JT, UK h Institute of Zoology, Zoological Society of London, Regent’s Park, London NW1 4RY, UK Received 26 July 2005; revised 26 June 2006; accepted 31 August 2006 Available online 23 September 2006 Abstract Phylogenetic reconstructions of relations within the phylum Nematoda are inherently diYcult but have been advanced with the intro- duction of large-scale molecular-based techniques. However, the most recent revisions were heavily biased towards terrestrial and para- sitic species and greater representation of clades containing marine species (e.g. -
Animal Biodiversity: an Outline of Higher-Level Classification and Survey of Taxonomic Richness
Title Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness Authors ZHI-QIANG ZHANG Publication date 2011/12/23 Journal name Zootaxa Volume 3148 Pages 1–237 Description Edited open-access book providing the total numbers of described species of animal phyla and an outline of the most updated higher classification to the family level for many groups. Chapters contributed by a team of over 100 specialists. An essential reference for those interested in biodiversity and animal classification. Zootaxa 3148: 1–237 (2011) ISSN 1175-5326 (print edition) www.mapress.com/zootaxa/ Monograph ZOOTAXA Copyright © 2011 · Magnolia Press ISSN 1175-5334 (online edition) ZOOTAXA 3148 Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness ZHI-QIANG ZHANG (ED.) New Zealand Arthropod Collection, Landcare Research, Private Bag 92170, Auckland, New Zealand; [email protected] Magnolia Press Auckland, New Zealand Accepted: published: 23 Dec. 2011 ZHI-QIANG ZHANG (ED.) Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness (Zootaxa 3148) 237 pp.; 30 cm. 23 Dec. 2011 ISBN 978-1-86977-849-1 (paperback) ISBN 978-1-86977-850-7 (Online edition) FIRST PUBLISHED IN 2011 BY Magnolia Press P.O. Box 41-383 Auckland 1346 New Zealand e-mail: [email protected] http://www.mapress.com/zootaxa/ © 2011 Magnolia Press All rights reserved. No part of this publication may be reproduced, stored, transmitted or disseminated, in any form, or by any means, without prior written permission from the publisher, to whom all requests to reproduce copyright material should be directed in writing.